1. Structure of Water
Covalently bound
Polar molecule

2. Hydrogen bonding
Occurs between Hydrogen of one water molecule with Oxygen of another
One molecule may make Hydrogen bonds to 4 other molecules
Weak and transient bonding (1/20th as strong as a covalent bond)

3. Cohesion/Adhesion Water molecules bond together (cohesion)
Allows capillary flow of water
Allows surface tension
Water molecules bond to other surfaces (adhesion)
Allows water to cling to vertical surfaces

4. Thermodynamics of Water
Water requires a lot of energy to heat it
Buffers temperature of ponds, lakes, oceans and organisms
1 cal=the energy to raise one gram of water one degree
Evaporation of water results in cooling of surfaces
Most active molecules become vapor leaving a less active environment

5. Expansion upon Freezing
Hydrogen bonds form lattice structure near 4°C
Results in decrease in density (10%)
Ice floats on surface of water
Prevents permanent freezing of bodies of water

6. Water as a solvent
Can dissolve substances with ionic or polar properties by interaction with charged regions
Hydrophilic=substance that will be dissolved in or wet by water (sugar, cotton)
Hydrophobic=substance that will not dissolve in water and repels water (oil, polystyrene)
Allows cells to contain many substances in solution
Chemicals tend to be more reactive in solution

7. Dissociation of Water Molecules randomly dissociate into OH- and H+
Amount of H+ in water determines acidity
High [H+]=acidic, Low [H+] =basic
pH =-log[H+] pH 7 is neutral,ph<7 is acidic, ph>7 is basic
Most biological systems are between pH 6 and 8
Buffers are weak acids or bases that tend to keep pH of a system near neutral conditions

8. 2H2O Hydronium ion (H3O+) Hydroxide ion (OH–)
Fig. 3-UN2 H H O O O H O H H H H H
2H2O
Hydronium
ion (H3O+)
Hydroxide
ion (OH–)

9. Organic Molecules Have Carbon as base
Carbon has four electrons in outer shell and this allows for many possible bonding configurations

10. Valence revisited
Hydrogen
(valence = 1)
Oxygen
(valence = 2)
Nitrogen
(valence = 3)
Carbon
(valence = 4) H O N C
The number of electrons in the outer shell determines how many bonds an atom may take part in
Valence=(8-# e in outer shell)
Examples
Carbon (8-4)=valence of 4

11. Bond number
Molecular structures are often drawn showing bonds as a line segment
The number of bonds around an atom should equal the valence number for the atom
If number differs then that portion of the molecule will be charged

12. Variations in Structure 1
Carbon-based molecules can vary in:
Chain length
Chain branching
Double or Triple bond position
Chain versus ring configuration

13. Variations in Structure 2
Can also differ as:
Structural isomers
Same composition but different bond arrangement
Geometric isomers
Functional groups are bound at different positions
Cis versus Trans
Enantiomers
Same functional groups but bound around carbon in different orientation
D versus L
One enantiomer of a molecule is frequently acitve while the other is inactive

14. Figure 4.10 Some biologically important chemical groups
Fig. 4-10a
CHEMICAL
GROUP
Hydroxyl
Carbonyl
Carboxyl
STRUCTURE
(may be written HO—)
In a hydroxyl group (—OH), a
hydrogen atom is bonded to an
oxygen atom, which in turn is
bonded to the carbon skeleton of
the organic molecule. (Do not
confuse this functional group
with the hydroxide ion, OH–.)
The carbonyl group ( CO)
consists of a carbon atom
joined to an oxygen atom by a
double bond.
When an oxygen atom is
double-bonded to a carbon
atom that is also bonded to
an —OH group, the entire
assembly of atoms is called
a carboxyl group (—COOH).
NAME OF COMPOUND
Alcohols (their specific names
usually end in -ol)
Ketones if the carbonyl group is
within a carbon skeleton
Carboxylic acids, or organic
acids
Aldehydes if the carbonyl group
is at the end of the carbon
skeleton
EXAMPLE
Ethanol, the alcohol present in
alcoholic beverages
Acetone, the simplest ketone
Acetic acid, which gives vinegar
its sour taste
Figure 4.10 Some biologically important chemical groups
Propanal, an aldehyde
FUNCTIONAL
PROPERTIES
Is polar as a result of the
electrons spending more time
near the electronegative
oxygen atom.
A ketone and an aldehyde may
be structural isomers with
different properties, as is the
case for acetone and propanal.
Has acidic properties
because the covalent bond
between oxygen and hydrogen
is so polar; for example,
Can form hydrogen bonds with
water molecules, helping
dissolve organic compounds
such as sugars.
These two groups are also
found in sugars, giving rise to
two major groups of sugars:
aldoses (containing an
aldehyde) and ketoses
(containing a ketone).
Acetic acid
Acetate ion
Found in cells in the ionized
form with a charge of 1– and
called a carboxylate ion (here,
specifically, the acetate ion).

15. Figure 4.10 Some biologically important chemical groups
Fig. 4-10b
CHEMICAL
GROUP
Amino
Sulfhydryl
Phosphate
Methyl
(may be
written HS—)
STRUCTURE
The amino group
(—NH2) consists of a
nitrogen atom bonded
to two hydrogen atoms
and to the carbon skeleton.
The sulfhydryl group
consists of a sulfur atom
bonded to an atom of
hydrogen; resembles a
hydroxyl group in shape.
In a phosphate group, a
phosphorus atom is bonded to
four oxygen atoms; one oxygen
is bonded to the carbon skeleton;
two oxygens carry negative
charges. The phosphate group
(—OPO32–, abbreviated ) is an
ionized form of a phosphoric acid
group (—OPO3H2; note the two
hydrogens).
A methyl group consists of a
carbon bonded to three
hydrogen atoms. The methyl
group may be attached to a
carbon or to a different atom. P
NAME OF
COMPOUND
Amines
Thiols
Organic phosphates
Methylated compounds
EXAMPLE
Glycine
Glycerol phosphate
Because it also has a
carboxyl group, glycine
is both an amine and
a carboxylic acid;
compounds with both
groups are called
amino acids.
Cysteine
In addition to taking part in
many important chemical
reactions in cells, glycerol
phosphate provides the
backbone for phospholipids,
the most prevalent molecules in
cell membranes.
5-Methyl cytidine
Cysteine is an important
sulfur-containing amino
acid.
5-Methyl cytidine is a
component of DNA that has
been modified by addition of
the methyl group.
Figure 4.10 Some biologically important chemical groups
FUNCTIONAL
PROPERTIES
Acts as a base; can
pick up an H+ from
the surrounding
solution (water, in
living organisms).
Two sulfhydryl groups
can react, forming a
covalent bond. This
“cross-linking” helps
stabilize protein
structure.
Contributes negative charge
to the molecule of which it is
a part (2– when at the end of
a molecule; 1– when located
internally in a chain of
phosphates).
Addition of a methyl group
to DNA, or to molecules
bound to DNA, affects
expression of genes.
Arrangement of methyl
groups in male and female
sex hormones affects
their shape and function.
Cross-linking of
cysteines in hair
proteins maintains the
curliness or straightness
of hair. Straight hair can
be “permanently” curled
by shaping it around
curlers, then breaking
and re-forming the
cross-linking bonds.
Has the potential to react
with water, releasing energy.
(nonionized)
(ionized)
Ionized, with a
charge of 1+, under
cellular conditions.